Elucidating Events within the Black Box of Enzyme Catalysis in Energy Metabolism: Insights into the Molecular Mechanism of ATP Hydrolysis by F(1)-ATPase

Oxygen exchange reactions occurring at β-catalytic sites of the F(O)F(1)-ATP synthase/F(1)-ATPase imprint a unique record of molecular events during the catalytic cycle of ATP synthesis/hydrolysis. This work presents a new theory of oxygen exchange and tests it on oxygen exchange data recorded on ATP hydrolysis by mitochondrial F(1)-ATPase (MF(1)). The apparent rate constant of oxygen exchange governing the intermediate Pi–HOH exchange accompanying ATP hydrolysis is determined by kinetic analysis over a ~50,000-fold range of substrate ATP concentration (0.1–5000 μM) and a corresponding ~200-fold range of reaction velocity (3.5–650 [moles of Pi/{moles of F(1)-ATPase}(−1) s(−1)]). Isotopomer distributions of [(18)O]Pi species containing 0, 1, 2, and 3 labeled oxygen atoms predicted by the theory have been quantified and shown to be in perfect agreement with the experimental distributions over the entire range of medium ATP concentrations without employing adjustable parameters. A novel molecular mechanism of steady-state multisite ATP hydrolysis by the F(1)-ATPase has been proposed. Our results show that steady-state ATP hydrolysis by F(1)-ATPase occurs with all three sites occupied by Mg-nucleotide. The various implications arising from models of energy coupling in ATP synthesis/hydrolysis by the ATP synthase/F(1)-ATPase have been discussed. Current models of ATP hydrolysis by F(1)-ATPase, including those postulated from single-molecule data, are shown to be effectively bisite models that contradict the data. The trisite catalysis formulated by Nath’s torsional mechanism of energy transduction and ATP synthesis/hydrolysis since its first appearance 25 years ago is shown to be in better accord with the experimental record. The total biochemical information on ATP hydrolysis is integrated into a consistent model by the torsional mechanism of ATP synthesis/hydrolysis and shown to elucidate the elementary chemical and mechanical events within the black box of enzyme catalysis in energy metabolism by F(1)-ATPase.